Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,411,782	A→G	10.2%	K99R (AAG→AGG)	PP_5551 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,411,782	0	A	G	10.2%	127.5 / 6.1	49	K99R (AAG→AGG)	PP_5551	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (15/29);  new base G (2/3);  total (17/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.52e-01

CAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATGGGATAGGGCGGGTGAAGAGTTTTCCCTAATCAGGCGTCATATCACAGGCGGGCATTTTGAAGTTCTTAGCCGTGCTGCGCTATCGCCCAAT  >  NC_002947/3411638‑3411921                                                                                                                                                 |                                                                                                                                            cAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAg                                                                                                                                            <  1:37744/146‑1 (MQ=255) cAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAg                                                                                                                                            <  7:52225/146‑1 (MQ=255) cAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAg                                                                                                                                            <  6:42878/146‑1 (MQ=255)       aagaGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTTTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGAc                                                                                                                                   <  5:175231/149‑1 (MQ=255)            cTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGAGCTTTc                                                                                                                              >  7:280429/1‑149 (MQ=255)              tGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCgg                                                                                                                            >  1:122801/1‑149 (MQ=255)               gCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCg                                                                                                                             <  3:317674/147‑1 (MQ=255)                       cAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTc                                                                                                                   >  5:45165/1‑149 (MQ=255)                         aTCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCtt                                                                                                                 <  4:84043/149‑1 (MQ=255)                            gCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAGGGTAAAGGACCTTTCGGCAAGATGTCTTGAg                                                                                                              <  5:178053/149‑1 (MQ=255)                              aaGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGta                                                                                                            >  6:320757/1‑149 (MQ=255)                                gCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGta                                                                                                            >  7:37074/1‑147 (MQ=255)                                      cTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCtt                                                                                                    <  4:170658/149‑1 (MQ=255)                                         ggAAAAGATTACGCAAGAATAACACGAGCTGTTGTCTGTCAATCATCAGTATTGGACGAGTGACGGCCGTGAGCGCGATACTTCCGCCTTGATGCTAAAACTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCtttt                                                                                                  <  4:184034/148‑1 (MQ=255)                                              aGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATgg                                                                                            <  2:33235/149‑1 (MQ=255)                                              aGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATgg                                                                                            <  6:302416/149‑1 (MQ=255)                                               gATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATgg                                                                                            >  5:146806/1‑148 (MQ=255)                                                 ttACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATGGGa                                                                                          <  3:43424/148‑1 (MQ=255)                                                     tCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATGGGATAggg                                                                                     >  3:185561/1‑149 (MQ=255)                                                       aaGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATGGGATAGGGCg                                                                                   >  5:302099/1‑149 (MQ=255)                                                        aGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATGGGATAGGGCgg                                                                                  <  6:45165/149‑1 (MQ=255)                                                        aGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATGGGATAGGGCgg                                                                                  <  8:215751/149‑1 (MQ=255)                                                              aGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATGGGATAGGGCGGGTGaa                                                                             <  3:63713/148‑1 (MQ=255)                                                               gACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCTCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATGGGATAGGGCGGGTGAaga                                                                           <  3:247724/149‑1 (MQ=255)                                                               gACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATg                                                                                             >  6:269338/1‑131 (MQ=255)                                                               gACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATGGGATAGGGCGGGTGAaga                                                                           <  6:245507/149‑1 (MQ=255)                                                                  gAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATGGGATAGGGCGGGTGAAGAGtt                                                                        <  1:47619/149‑1 (MQ=255)                                                                        ttGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATGGGATAGGGCGGGTGAAGAGTTTTccc                                                                   <  6:146806/148‑1 (MQ=255)                                                                        ttGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATGGGATAGGGCGGGTGAAGAGTTTTcc                                                                    <  2:261787/147‑1 (MQ=255)                                                                        ttGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATGGGATAGGGCGGGTGAAGAGTTTTcc                                                                    <  2:137643/147‑1 (MQ=255)                                                                                  ctctTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAGGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTa                                                                                               >  6:114000/1‑110 (MQ=255)                                                                                  ctctTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAGGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTa                                                                                               <  5:114000/110‑1 (MQ=255)                                                                                  ctctTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAGGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTa                                                                                               <  5:113998/110‑1 (MQ=255)                                                                                  ctctTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAGGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTa                                                                                               >  6:113998/1‑110 (MQ=255)                                                                                       cAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATGGGATAGGGCGGGTGAAGAGTTTTCCCTAATCAGGCGTCat                                                     <  4:185561/147‑1 (MQ=255)                                                                                         gTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATGGGATAGGGCGGGTGAAGAGTTTTCCCTAATCAGGCGTCATATca                                                 >  8:155424/1‑149 (MQ=255)                                                                                              gtaCGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATGGGATAGGGCGGGTGAAGAGTTTTCCCTAATCAGGCGTCATATCACAgg                                             <  4:276211/146‑1 (MQ=255)                                                                                                aCGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATGGGATAGGGCGGGTGAAGAGTTTTCCCTAATCAGGCGTCATATCACAGGCgg                                          <  6:302099/149‑1 (MQ=255)                                                                                                  gAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTATATGGGATAGGGCGGGTGAAGAGTTTTCCCTAATCAGGCGTCATATCACAGGCggg                                         >  4:32165/1‑148 (MQ=255)                                                                                                          gCCGTGAGGGCCCTACTTCCGCCTTGAAGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATGGGATAGGGCGGGTGAAGAGTTTTCCCTAATCAGGCGTCATATCACAGGCGGGCATTTTGaa                                <  8:280429/149‑1 (MQ=255)                                                                                                              tGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATGGGATAGGGCGGGTGAAGAGTTTTCCCTAATCAGGCGTCATATCACAGGCGGGCATTTTGAAGTTc                            <  3:32165/149‑1 (MQ=255)                                                                                                                  ggCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATGGGATAGGGCGGGTGAAGAGTTTTCCCTAATCAGGCGTCATATCACAGGCGGGCATTTTGAAGTTCTTAg                        >  7:217067/1‑149 (MQ=255)                                                                                                                  ggCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATGGGATAGGGCGGGTGAAGAGTTTTCCCTAATCAGGCGTCATATCACAGGCGGGCATTTTGAAGTTCTTAg                        <  2:6707/149‑1 (MQ=255)                                                                                                                              gCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATGGGATAGGGCGGGTGAAGAGTTTTCCCTAATCAGGCGTCATATCACAGGCGGGCATTTTGAAGTTCTTAGCCGTGCTgcgc             >  8:86862/1‑148 (MQ=255)                                                                                                                                    aTGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATGGGATAGGGCGGGTGAAGAGTTTTCCCTAATCAg                                                            <  6:313421/95‑1 (MQ=255)                                                                                                                                    aTGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATGGGATAGGGCGGGTGAAGAGTTTTCCCTAATCAg                                                            >  5:313421/1‑95 (MQ=255)                                                                                                                                    aTGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATGGGATAGGGCGGGTGAAGAGTTTTCCCTAATCAGGCGTCATATCACAGGCGGGCATTTTGAAGTTCTTAGCCGTGCTGCGCTATCGc       <  2:122801/148‑1 (MQ=255)                                                                                                                                       cTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATGGGATAGGGCGGGTGAAGAGTTTTCCCTAATCAGGCGTCATATCACAGGCGGGCATTTTGAAGTTCTTAGCCGTGCTGCGCTATCGCCCa    <  8:217067/148‑1 (MQ=255)                                                                                                                                        tAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATGGGATAGGGCGGGTGAAGAGTTTTCCCTAATCAGGCGTCATATCACAGGCGGGCATTTTGAAGTTCTTAGCCGTGCTGCGCTATCGCCCAAt  >  4:64920/1‑149 (MQ=255)                                                                                                                                                 |                                                                                                                                            CAAAAGAAGAGCTTGCGAAGGTCAATCGCAAGCTTCGCTTGGAAAAGATTACTCAAGATTTAGACGAGCTTTTGGCTGTCACTCTTCAGTATTGGACGAGTGACGGCCGTGAGGGCGCTACTTCCGCCTTGATGCTAAAAGTCAAGGTAAAGGACCTTTCGGCAAGATGTCTTGAGTATAGGTCTTTTCTATGGGATAGGGCGGGTGAAGAGTTTTCCCTAATCAGGCGTCATATCACAGGCGGGCATTTTGAAGTTCTTAGCCGTGCTGCGCTATCGCCCAAT  >  NC_002947/3411638‑3411921

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑